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Molecular dynamics simulation of histone H3 and H4 N-terminal tail conformation in the presence and absence of nucleosome core

100%

Zhang R. , Erler J. , Langowski J.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2014

tom Vol. 18, No 3

281--288

Histone N ( C )-terminal tails play an important role in chromatin remodeling and gene regulation. Posttranslational modifications ( PTM s) of histone tails are known to be correlated to distinct states of gene activity, but the molecular mechanism of these processes is largely unknown. PTM s alter the electrostatic environment and conformation of histone tails, as w ell as their interaction with other components. Here we performed extensiv e Replica Exchange Molecular Dynamics ( REMD ) simulations for the H 4 and H 3 tails, isolated and with inclusion of a nucleosome. Our results agree with the predictions of previous the oretical studies for the secondary structure of isolated tails, but show strong dependence on the force field used. In the presence of the nucleosome, the secondary structure of histone tails i s destabilized. Furthermore, H 4 K 16 is found to insert into the DNA minor groove, whereas the acetylated H 4 K 16 stays on the surface of DNA .

A novel approach for preventing esophageal stricture formation: olmesartan prevented apoptosis

84%

Dereli M. , Krazinski B. E. , Ayvaz S. , Aksu B. , Kanter M. , Uzun H. , Gelisgen R. , Umit C. H. , Inan M. , Basaran U. N. , Pul M.

Folia Histochemica et Cytobiologica

2014

tom 52

nr 1

DNA microarrays, a novel approach in studies of chromatin structure

84%

Widlak P.

Acta Biochimica Polonica

2004

tom 51

nr 1

The DNA microarray technology delivers an experimental tool that allows surveying expression of genetic information on a genome-wide scale at the level of single genes — for the new field termed functional genomics. Gene expression profiling — the primary application of DNA microarrays technology — generates monumental amounts of information concerning the functioning of genes, cells and organisms. However, the expression of genetic information is regulated by a number of factors that cannot be directly targeted by standard gene expression profiling. The genetic material of eukaryotic cells is packed into chromatin which provides the compaction and organization of DNA for replication, repair and recombination processes, and is the major epigenetic factor determining the expression of genetic information. Genomic DNA can be methylated and this modification modulates interactions with proteins which change the functional status of genes. Both chromatin structure and transcriptional activity are affected by the processes of replication, recombination and repair. Modified DNA microarray technology could be applied to genome-wide study of epigenetic factors and processes that modulate the expression of genetic information. Attempts to use DNA microarrays in studies of chromatin packing state, chromatin/DNA-binding protein distribution and DNA methylation pattern on a genome-wide scale are briefly reviewed in this paper.

Reconstitution of UV-damaged DNA into chromatin using Xenopus oocyte extracts

67%

Widlak P.

Acta Biochimica Polonica

1998

tom 45

nr 2

Chromatin was reconstituted in vitro using Xenopus oocyte extracts and plasmid DNA containing UV radiation-induced damage. Damaged DNA was assembled into minichromosomes with an efficiency similar to that of control, non-irradiated DNA. Oocyte extracts were competent to carry out DNA repair, which was elicited by nicking damaged templates followed by DNA synthesis during chromatin assembly. Newly synthesized DNA was efficiently reconstituted into nucleosomes.